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Acknowledgements Page Anchor’s author is Owen Feehan. Particular additional thanks to: ETH Zurich, the late Prof. Wilhelm Krek in whose lab the software originated for analyzing microscopy images. Many members of the Institute of Molecular Health Sciences who kindly helped in associated research and became the first...
Developer Guide - Getting started Page Key systems GitHub - hosts all source code, the website, and issues and projects. Amazon AWS - provides a build server build.anchoranalysis.org (on demand - suspended when not in use). Services running on the build-server include: Nexus Repository Server - to publish...
Developer Guide - Anchor distribution Page What is an Anchor distribution? An Anchor distribution is a folder which contains all the jars and configuration-files to run Anchor. It has the following structure: Folder Description bin/ anchor-launcher.jar and anchor-browser.jar and associated helper-applications lib/...
Developer Guide - Building Anchor Page Maven Anchor uses Apache Maven as a build tool. As a prior step, Maven should be installed locally, configured for the Anchor project. Assembly The anchor-assembly is a special module that doesn’t generate a .jar artifact, but rather assembles the output of other modules (artifacts) into...
Download Page Anchor can be downloaded as a distribution (zip or tar.gz). This must be unpacked into a directory, followed by setting some environment variables. Please download the latest version from GitHub. Warning: Anchor is currently only available pre-alpha, due to ongoing <a...
Installation Page Anchor is a command-line application, designed to be used with PowerShell / Command Prompt in Windows, Terminal in MacOS or any Linux shell. Quick Instructions Download, unzip, and add the bin/ directory to $PATH environmental variable....
Installation - Detailed Instructions Page Anchor is a command-line application, designed to be used with PowerShell / Command Prompt in Windows, Terminal in MacOS or any Linux shell. It should be added to the system’s PATH environmental variable. Steps 1. Download and unpack...
User Guide - Essentials Page ## Essentials of Anchor ### Experiments are inputs, task, outputs An experiment is *roughly-speaking* the execution of a **task** on **inputs** to produce **outputs**. ``` outputs = task(inputs) ``` Inputs are usually images (or images plus extras). Outputs can be images, text-files, CSVs, XML or any other file-type. {% include...
User Guide - BeanXML Page ## What is BeanXML? BeanXML is a type of XML used by Anchor to define experiments, configuration and many aspects of behaviour. It is flexible and extensible, and can easily be used with new types of plugins and other objects, as they are developed and added to Anchor. {% include...
User Guide - Command line Page ## Introduction Anchor can be used from the command-line as follows: ```shell anchor [options] [experimentFile.xml] ``` If an `experimentFile.xml` isn't specified, the [default experiment](/user_guide.html#defaultExperiment) is employed, with default *inputs*, *task*, *outputs*. ## Major options The **most important** command-line options are: | Option | Description| |----------|------------| | -h | Displays help...
User Guide - Supported image formats Page ## Images are diverse ### Image types We typically intuitively think of an image file as a digital photograph like a JPEG similar in appearance to human vision, containing a matrix of RGB pixels (three interdependent channels), or perhaps grayscale photographs (single channel). In reality, images come in much more...